LAMMPS (11 Aug 2017) clear units metal dimension 3 boundary p p p atom_style atomic lattice fcc 4.02484538406 Lattice spacing in x,y,z = 4.02485 4.02485 4.02485 region whole block 0 34.38829403573262 -68.78061291684931 68.78061291684931 0 4.02484538406 units box create_box 2 whole Created orthogonal box = (0 -68.7806 0) to (34.3883 68.7806 4.02485) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 68.78061291684931 INF INF units box lattice fcc 4.02484538406 orient x 8 -3 0 orient y 3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1818 5.1818 4.02485 create_atoms 1 region upper Created 586 atoms group upper type 1 586 atoms in group upper mass 1 26.981538 displace_atoms upper move 3.844801685392889 0 0.3333333333333333 region lower block INF INF -68.78061291684931 0.0 INF INF units box lattice fcc 4.02484538406 orient x 8 3 0 orient y -3 8 0 orient z 0 0 1 Lattice spacing in x,y,z = 5.1818 5.1818 4.02485 create_atoms 2 region lower Created 586 atoms group lower type 2 586 atoms in group lower displace_atoms lower move -3.844801685392889 0 -0.3333333333333333 mass 2 26.981538 pair_style kim LAMMPSvirial EAM_Dynamo_Winey_Kubota_Al__MO_149316865608_004 pair_coeff * * Al Al neighbor 2.0 bin neigh_modify delay 10 check yes delete_atoms overlap 2.01242269203 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 9 33 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Deleted 18 atoms, new total = 1154 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard Per MPI rank memory allocation (min/avg/max) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3038.0851 0 -3038.0851 -2367.4523 322 0 -3045.3393 0 -3045.3393 -5152.1936 Loop time of 2.37262 on 1 procs for 322 steps with 1154 atoms 100.0% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3038.08506074 -3045.3392833 -3045.3392833 Force two-norm initial, final = 9.22468 2.92413e-06 Force max component initial, final = 2.57748 7.72365e-07 Final line search alpha, max atom move = 1 7.72365e-07 Iterations, force evaluations = 322 641 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3319 | 2.3319 | 2.3319 | 0.0 | 98.29 Neigh | 0.0030351 | 0.0030351 | 0.0030351 | 0.0 | 0.13 Comm | 0.022164 | 0.022164 | 0.022164 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01548 | | | 0.65 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8532 ave 8532 max 8532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136898 ave 136898 max 136898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136898 Ave neighs/atom = 118.629 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 5.006 | 5.006 | 5.006 Mbytes Step Temp E_pair E_mol TotEng Press Volume 322 0 -3045.3393 0 -3045.3393 -5152.1936 19039.515 1322 0 -3045.515 0 -3045.515 -633.56478 18929.471 Loop time of 7.99745 on 1 procs for 1000 steps with 1154 atoms 99.9% CPU use with 1 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -3045.3392833 -3045.51499212 -3045.51499214 Force two-norm initial, final = 84.955 0.0111623 Force max component initial, final = 62.2026 0.00728024 Final line search alpha, max atom move = 0.450166 0.00327732 Iterations, force evaluations = 1000 1997 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6487 | 7.6487 | 7.6487 | 0.0 | 95.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.063413 | 0.063413 | 0.063413 | 0.0 | 0.79 Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2853 | | | 3.57 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8695 ave 8695 max 8695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136810 ave 136810 max 136810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136810 Ave neighs/atom = 118.553 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 compute csym all centro/atom fcc compute csymsum all reduce sum c_csym compute eng all pe/atom compute eatoms all reduce sum c_eng compute distance all pair/local dist compute mindist all reduce min c_distance reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.145 | 5.145 | 5.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3045.515 0 -3045.515 -633.56478 Loop time of 0 on 1 procs for 0 steps with 1154 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0 | | | 0.00 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8739 ave 8739 max 8739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136903 ave 136903 max 136903 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136903 Ave neighs/atom = 118.633 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms c_mindist c_csymsum run 0 WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 5.145 | 5.145 | 5.145 Mbytes Step PotEng Lx Ly Lz Press Pxx Pyy Pzz c_eatoms c_mindist c_csymsum 0 -3045.515 34.302843 137.56123 4.0115512 -633.56478 -0.61466277 -1899.6941 -0.38560301 -3045.515 2.541626 634.069 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1154 atoms 0.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1154 ave 1154 max 1154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8739 ave 8739 max 8739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136903 ave 136903 max 136903 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 161120 ave 161120 max 161120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161120 Ave neighs/atom = 139.619 Neighbor list builds = 0 Dangerous builds = 0 variable total_energy equal c_eatoms print "${total_energy}" file output/dump_041.1121/energy.out -3045.51499214323 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_041.1121/numatoms.out 1154 variable minimum_distance equal c_mindist print "${minimum_distance}" file output/dump_041.1121/mindistance.out 2.5416259817651 write_dump all cfg output/dump_041.1121/dump_post.cfg mass type xs ys zs id type xs ys zs c_csym c_eng modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_041.1121/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:10